BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 010798
(501 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3MKT|A Chain A, Structure Of A Cation-Bound Multidrug And Toxin Compound
Extrusion (Mate) Transporter
pdb|3MKT|B Chain B, Structure Of A Cation-Bound Multidrug And Toxin Compound
Extrusion (Mate) Transporter
pdb|3MKU|A Chain A, Structure Of A Cation-Bound Multidrug And Toxin Compound
Extrusion (Mate) Transporter
pdb|3MKU|B Chain B, Structure Of A Cation-Bound Multidrug And Toxin Compound
Extrusion (Mate) Transporter
Length = 460
Score = 75.1 bits (183), Expect = 9e-14, Method: Compositional matrix adjust.
Identities = 94/444 (21%), Positives = 177/444 (39%), Gaps = 24/444 (5%)
Query: 51 LVRLAAPAVFVYLINNLMSLSTRVFCGHLGNLELAAASLGNS---GIQLFAYGLMLGMGS 107
L++LA P + + M + G + +++AA S+ S LF GL++
Sbjct: 14 LIKLATPVLIASVAQTGMGFVDTIMAGGVSAIDMAAVSIAASIWLPSILFGVGLLM---- 69
Query: 108 AVETLCGQAYGAGRYEMLGVYMQRATFVLLATGVPVMMVYIFCKPMLILLGESTAVASAA 167
A+ + Q GAGR + + + + L VP++ V + ++ + A+A+
Sbjct: 70 ALVPVVAQLNGAGRQHKIPFEVHQGLILALLVSVPIIAVLFQTQFIIRFMDVEEAMATKT 129
Query: 168 ALFVYGLIPQIFAYAVNFPIQKFLQAQSIVLPSAYISAATXXXXXXXXXXXXY-KFGA-- 224
+++ +I + AY + ++ F S+ P+ I Y KFGA
Sbjct: 130 VGYMHAVIFAVPAYLLFQALRSFTDGMSLTKPAMVIGFIGLLLNIPLNWIFVYGKFGAPE 189
Query: 225 -GLIGASLVLSLSWYIIVGAQFAYILMSDKCKH--TWTGFSVQAFSGICEFLKLSGSSAV 281
G +G + ++ ++I++ YI+ S + H + F + +L A
Sbjct: 190 LGGVGCGVATAIVYWIMLLLLLFYIVTSKRLAHVKVFETFHKPQPKELIRLFRLGFPVAA 249
Query: 282 MLCLETWYFQILVLIAGLLDNPELALDSLSVCMAVSGLLFMVSVGFNAAASVRVSNELGA 341
L E F ++ L+ L + +A + V + S L+FM + AA S+RV ++LG
Sbjct: 250 ALFFEVTLFAVVALLVAPLGSTVVA--AHQVALNFSSLVFMFPMSIGAAVSIRVGHKLGE 307
Query: 342 GNPKXXXXXXXXXXXXXXXXXXXXXXXXLALRHVISYAFTSGEVVANAVSEXXXXXXXXX 401
+ K + R I+ +T +VV +
Sbjct: 308 QDTKGAAIAANVGLMTGLATACITALLTVLFREQIALLYTENQVVVALAMQLLLFAAIYQ 367
Query: 402 XXNGVQPVLSGVAVGCGWQAFVAYVNIACYYIVGIPLGCLLGF-----KFNFGAKGIWSG 456
+ VQ V +G G + + Y+++G+P G +LG + GAKG W G
Sbjct: 368 CMDAVQVVAAGSLRGYKDMTAIFHRTFISYWVLGLPTGYILGMTNWLTEQPLGAKGFWLG 427
Query: 457 MIGGTAMQTII----LLWVTIRTD 476
I G + ++ L W+ ++D
Sbjct: 428 FIIGLSAAALMLGQRLYWLQKQSD 451
>pdb|4HUK|A Chain A, Mate Transporter Norm-ng In Complex With Tpp And Monobody
pdb|4HUL|A Chain A, Mate Transporter Norm-ng In Complex With Cs+ And Monobody
pdb|4HUM|A Chain A, Mate Transporter Norm-ng In Complex With Ethidium And
Monobody
pdb|4HUN|A Chain A, Mate Transporter Norm-ng In Complex With R6g And Monobody
Length = 459
Score = 34.3 bits (77), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 1/75 (1%)
Query: 47 ELKLLVRLAAPAVFVYLINNLMSLSTRVFCGHLGNLELAAASLGNSGIQLFAYGLMLGMG 106
E++LL LA P + + + V G G +LAA +LG+S Y +G+
Sbjct: 12 EIRLLTALALPMLLAQVAQVGIGFVDTVMAGGAGKEDLAAVALGSSAFAT-VYITFMGIM 70
Query: 107 SAVETLCGQAYGAGR 121
+A+ + Q YGAG+
Sbjct: 71 AALNPMIAQLYGAGK 85
Score = 32.7 bits (73), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 33/179 (18%), Positives = 64/179 (35%), Gaps = 9/179 (5%)
Query: 312 VCMAVSGLLFMVSVGFNAAASVRVSNELGAGNPKXXXXXXXXXXXXXXXXXXXXXXXXLA 371
V +++SG+L+M+ +A +VR+ LG +
Sbjct: 281 VGISLSGILYMIPQSVGSAGTVRIGFSLGRREFSRARYISGVSLVSGWVLAVITVLSLVL 340
Query: 372 LRHVISYAFTSGEVVANAVSEXXXXXXXXXXXNGVQPVLSGVAVGCGWQAFVAYVNIACY 431
R ++ + V + S + Q + S G +++ A +
Sbjct: 341 FRSPLASMYNDDPAVLSIASTVLLFAGLFQPADFTQCIASYALRGYKVTKVPMFIHAAAF 400
Query: 432 YIVGIPLGCLLGFKFNFGAKGIWSGMIGGTAMQTIILLWVTIRTDWKKEVEKAKMRLDK 490
+ G+ G LL ++F+ G G W+ +I + + L+W +EK M L K
Sbjct: 401 WGCGLLPGYLLAYRFDMGIYGFWTALIASLTIAAVALVWC---------LEKYSMELVK 450
>pdb|4ECL|A Chain A, Crystal Structure Of The Cytoplasmic Domain Of Vancomycin
Resistance Serine Racemase Vantg
pdb|4ECL|B Chain B, Crystal Structure Of The Cytoplasmic Domain Of Vancomycin
Resistance Serine Racemase Vantg
pdb|4ECL|C Chain C, Crystal Structure Of The Cytoplasmic Domain Of Vancomycin
Resistance Serine Racemase Vantg
pdb|4ECL|D Chain D, Crystal Structure Of The Cytoplasmic Domain Of Vancomycin
Resistance Serine Racemase Vantg
Length = 374
Score = 29.6 bits (65), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 43/86 (50%), Gaps = 11/86 (12%)
Query: 238 YIIVGAQFAYILMSDKCKHTWTGFS---VQAFSGICEFLKLSGSSAVMLCLETWYFQILV 294
+I V F ++ +D + F+ + +F + ++LK SG + + +++ Y
Sbjct: 151 HIKVAGIFTHLCAADSLEENDVAFTNKQIGSFYKVLDWLKSSGLNIPKVHIQSSY----- 205
Query: 295 LIAGLLDNPELALDSLSVCMAVSGLL 320
GLL+ PEL D + V +A+ G+L
Sbjct: 206 ---GLLNYPELECDYIRVGVALYGVL 228
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.325 0.137 0.414
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,134,007
Number of Sequences: 62578
Number of extensions: 422542
Number of successful extensions: 1010
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1001
Number of HSP's gapped (non-prelim): 6
length of query: 501
length of database: 14,973,337
effective HSP length: 103
effective length of query: 398
effective length of database: 8,527,803
effective search space: 3394065594
effective search space used: 3394065594
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (25.0 bits)